City of Bones, Alternative Ending
by GirlInHerOwnWorld
Summary: It starts when Simon has just stormed out after seeing Clary and Jace kiss and he reveals that he is in love with her.
1. Chapter 1

**Okay, so this is my first fanfic. I hope you guys like it, I just thought Clary's reaction was like she just shrugged the incident off. It begins after Simon has left. **

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><p><strong>Clary POV<strong>

Clary sat on her bed, shock covered her face and ran through her body. She felt numb and alone, her whole life had been turned upside down in a week. Not even bothering to change into her pajamas she turned off her light and curled into a ball on her bed.

Her mother, missing. Luke, didn't want anything to do with her. Simon, was more than angry. She was alone with strangers, and Jace had gone back to being his normal arrogant, sarcastic self. Sighing she rolled over and tried to get some sleep, willing herself not to think about that kiss of all things.

It had been three hours and still sleep was out of reach. Clary had counted every crack on the roof, every line on the floor over and over. Deciding that she couldn't take it anymore she got out of bed. After changing into her pajama shorts and singlet she wanted a walk. Needing to clear her mind she began wandering the halls of the institute. So deep in her thoughts Clary hadn't even realised where she was headed until she was standing in front of Jace's room. Unsure what to do next she placed her hand on his door and stood there for a moment as if it could bring her closer to his touch. Squeezing her eyes shut she turned and ran back down the hall. She kept running until she found the stairs to the greenhouse, quietly she climbed up them. Walking through silently she found Hodge had left. She sat where she had been just a few hours ago and let it all out.

**Jace POV**

Jace hadn't been able to sleep. He heard the slow approaching footsteps and saw the movement under his door. He held his breath hoping whoever it was would think he was asleep and leave him alone. He had a pretty good idea who but was determined not to respond. It was crazy how one girl could have such an effect on him. Every time he saw her, his heart beat faster. All he wanted to do was hold her close, to protect her. After a moment the figure moved and began running away, the footsteps grew fainter.

Jace jumped out of bed and opened his door but she was gone. Unsure why he began to follow her. When he reached the greenhouse steps he hadn't been able to clear his thoughts of Clary. Knowing that Hodge would be in bed by now he just wanted to see her. When he entered the greenhouse he froze, there was a quiet sobbing noise coming from inside. He spotted Clary lying where they had their picnic, she was shaking and tears rolled of her pink cheeks. He walked over to her,

"Let me guess-" Jace started in a sarcastic voice. She looked up then turned away quickly but not before he saw the hurt on her face. He stopped talking and sat down next to her, as he realised she really was really hurting.

"Clary?" He whispered, stroking her hair. "Are you OK?" She looked up at him and he saw the heartbroken look on her face. It broke his heart to see how much pain she was in, especially since it was his fault. Clary just stared up at him, her sobbing had stopped but tears kept falling. He held her as if he could take away all her pain and suffering onto himself.

"Jace." She whispered in a shaky voice, "What are you doing?". He looked into her eyes, what was he doing? To love was to destroy. Yet Jace couldn't let Clary go, he should have left then but instead he held her tighter.

"I don't know." He whispered, his voice slightly uneven. He tried to gain control but let his guard down the instant she leaned up and kissed him. It was soft and sweet and caught him by surprise.

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><p><strong>Please review and let me know what you think. :) If people like it I'll write more, this was just something I started in Research Project.<strong>

**- Love Chrissy**


	2. Chapter 2

Sorry about the slow upload. I have been busy with school ect. Let me know what you think, the more reviews the more motivated I'll be.

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><p><strong>Clary POV<strong>

Clary didn't want sweet. She needed a distraction and more importantly she needed him, to feel like someone cared. She reached up and pulled him against her as the kiss grew harder and more intense. A small voice in the back of her head warned her that he was probably just using her and that he did this with a lot of girls. She pushed that thought aside and pulled him against her harder, the kiss had gone beyond soft it had turned to what she thought was passion. Jace laid her gently on the ground without breaking contact.

Clary grabbed his shirt and unbuttoned it. His hand moved down her ribs to her waist while his other arm pulled her harder against him. She had never felt anything like this before, it was amazing and felt so right. She started moving her hands across his back, fingers tracing the permanent scars left behind from a life of fighting, war and pain. He shuddered pressing harder against her and let out a quiet moan. Clary's hands moved down his ribs and to his belt buckle.

**Jace POV **

Jace felt amazing. Sure he had hooked-up with other girls before but never like this. He had always wanted them, got them, then lost interest but with Clary it was entirely different, he never wanted to let her go. Clary started playing with his belt buckle, all of a sudden she was undoing it. Jace froze.

"Clary?" Jace whispered, slightly panting.

"Mmm?" Clary replied.

"What are you doing?"

'What do you think?" she said with a giggle.

"Don't." He whispered back, Clary's face went blank. "It's not that I don't want to believe me," He smiled and stroked her face. "just you're upset and I don't want to take advantage of that." Clary looked away. "What's wrong?" Jace asked.

"I'm sorry.. I-I didn't.." She stuttered, then pushed Jace off of her and ran out of the room leaving Jace sitting there speechless.


	3. Chapter 3

**Jace POV **

By the time Jace had reached the bottom of the stairs Clary was nowhere to be seen. He wanted to make sure she was ok, to reassure her but thought it would be best not to. _Damn! _he thought _To love is to destory, if not me then her.._

He went back to his room quietly.

**Clary POV **

Clary didn't want to go back to her room in case Jace came looking for her. She decided to get dressed and pack her bag. Now that Simon was angry at her, she had nowhere to go she just felt as if she should leave. They didn't really care about her or her mother just there precious shadowhunter things. They probably wouldn't even notice her gone or care if they did.

Clary quietly entered the elevator and pressed the down button. She silently cursed herself for the noise it made taking her down.

**Jace POV **

Jace thought he heard the elevator start up, his heart missed a beat but instead of getting up he decided to roll over and try to get some sleep.

**Clary POV **

Clary walked silently past the pews and to the door. She opened it and stepped out into the New York night..


	4. Chapter 4

**I apologise for the ****_very _****long wait. I didn't have access to my account for a while and then I forgot. Again, I'm sorry and I hope you enjoy!**

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><p><strong>Clary POV <strong>

It was cold out on the streets, but Clary didn't care, she kept walking. She had no idea where she might end up, but she forced herself to keep moving forward instead of running back. She knew deep down she would have to eventually return, she couldn't survive on the streets for long.

She walked absent mindedly for a while before she recognised where she was. She was three blocks away from what use to be her home. Even after all the terrible things that had happened and the possible danger that lurked there she couldn't help, but go home.

It was really early in the morning by the time Clary entered her apartment. She quietly looked checked out the place making sure she was alone before collapsing in her empty bedroom. She was so exhausted that she immediately fell asleep.

**Jace POV **

Jace nervously walked toward the kitchen wondering what the day would hold. As he got closer he made sure his expression was neutral. Just before he was about to stride in he stopped, he could hear Izzy and Alec talking.

"Who cares," Alec said "she is just some stupid little girl. If she wants to go let her, there is no point in tracking her down if she doesn't want to be here." He sounded annoyed.

"Alec, it's more then that." Izzy said "You know she has no home, and what about Jace?"

"He doesn't need her, she just gets him hurt." Jace had heard enough and stormed into the kitchen.

"What, are you talking about?" He asked. Izzy and Alec looked up where Izzy seemed worried Alec looked annoyed.

"Umm, Clary has gone" Izzy said quietly while playing with her fingers. Jace looked at her confused.

"What do you mean gone?"

"I mean, she isn't anywhere, all her stuff is gone." She said. Jace remembered the sound of the elevator, _That must of been her leaving you idiot! _He thought and looked to Alec.

"Don't worry about her, she has probably gone to stay with friends. She isn't our problem anymore." Alec said. Jace glared at him and walked closer.

"She is one of us," he said in a low, fierce voice "she needs our help. She has no home, Valentine kidnapped her mother and she is probably the best chance we have at getting the cup." With that Jace stormed out and went to his room.

**Clary POV **

Clary woke to the sun streaming in through the window. She sat up and stretched, feeling stiff from sleeping on the floor. She sat there for a moment staring at the wall wondering what to do. She decided she would wait until dinner time before crawling back to the institute. There was nothing left in what was once her home. She continued to stare at the wall thinking about everything she had been through, everything she had lost in such a short amount of time.

She opened her bag and looked for a breakfast bar. After eating she decided to draw, that usually made her feel better. She sat and doodled, nothing would come to mind. She was about to give up when she noticed one of her doodles looked like a rune. She touched it and it glowed, leaving a warm feeling behind. This gave her an idea.

She grabbed the breakfast bar wrapper and drew it exactly. The rips in the right places, the way the sun reflected off the plastic, every detail. Then she placed the wrapper on top and drew the rune at the top of the page. Again it glowed and she watched with fascination as the wrapper became he drawing. She drew the rune again and reached in pulling the wrapper out again. Her excitement grew and she knew exactly where the mortal cup was. In a deck of painted cards, just downstairs...

**Jace POV **

Jace had gotten dressed and grabbed some weapons. He ran into Izzy and Alec at the elevator. "Where are you going?" Alec asked.

"Where do you think? I'm going to find Clary." Jace replied. He tried to pass by them but Alec pushed him back.

"Don't be stupid, call her or something. You have no idea where she is."

"I don't have her number." Jace replied and got into the elevator.

Izzy suggested ringing Simon to see if she was there. "Where would I get his number?" Jace growled.

Izzy simply lifted a piece of paper with a number scrawled across it. "Never underestimate me." She said with a smile.

"Fine," Jace said, "but you're calling him."

Izzy just smiled again, "No problem." She dialled the number. "Hello, Simon?" She said in a sweet voice. An irritated one answered. "I was just wondering if Clary was with you." Izzy continued. "All her stuff is gone and we didn't know where else she might go." She said panic colouring her voice. "She isn't there." She whispered.

Jace took the phone out of her hands. "Simon it's Jace, is there anywhere else she may of gone?" He asked.

"If she was upset she may of gone home, no matter how dangerous it is." Simon replied.

Jace paled and the panic hit him even harder. "She could be in a lot of danger, we'll head right over." He said.

"Wait for me." Simon pleaded.

"It is going to take long enough with public transport without having to wait for you." He snapped.

"I can drive." Simon interjected before he had time to slam the phone.

"We'll meet you out front." He said neutrally before hanging up.


	5. Chapter 5

**I don't have internet at home so I can't constantly upload, sorry. Also this is my first go at Fanfic so if you have any tips or advice please don't hesitate to tell me. Thank-you for your patience. **

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><p><strong>Clary POV<strong>

Clary gathered things back into her backpack and raced down the stairs. She pounded on Madame Dorothea's door three times before realizing that it was still early in the morning. Luckily for her Dorothea seemed to be a morning person. She opened the door with a bright smile. "Clary," she said in a clear ringing voice, "how lovely to see you again. Please come in."

"Thank-you Madame Dorothea." Clary replied as she followed her into the parlor.

"Now, what brings you back here child? Did you find the Mortal Cup?" She asked while pouring Clary a cup of tea.

"Not exactly," Clary began slowly, "but I know where it is." Madame Dorothea paused, then looked up at her wide eyed.

"Where?" She whispered.

"It is in this very room." Clary replied. Madame Dorothea's expression turned angry.

"Here? Are you accusing me of hiding the Mortal Cup!"She yelled, her cheeks turning red.

"No, that's not what I meant." Clary rushed, "I meant that my mother hid them here. Disguised as a gift." Clary explained while drawing out the Tarot cards. She picked up the one that seem to call to her then showed it to Madame Dorothea. Then she placed it on the table and sketched the rune in the top corner. As soon as it glowed she reached in and plucked the cup out. As soon as it left the card turned to ash. Clary's face lit up with excitement. She couldn't believe she had done it, and all on her own too.

"Oh, no."Madame Dorothea said while staring at the cup, "It's damaged, give it here and I'll fix it."Her eyes fastened intensely on the cup. Clary looked at it confused, it didn't look damaged. It looked exactly the same as it did in all the pictures. She looked up at Madame Dorothea, a sense of wrongness began to fill her. She slowly stood up and took a step back, in the direction of the front door.

"It's fine."She whispered in a shaky voice. At that Madame Dorothea's face twisted into anger. She stepped over to the portal door. "I don't need that, thanks."She said, the feeling of wrongness and dread almost crushing her. A twisted smile appeared on her face as she opened the portal door and chaos was unleashed.


	6. Chapter 6

**If you haven't already re-read the previous chapter I edited it. Hope you enjoy!**

**DISCLAIMER: I OBVIOUSLY DON'T OWN THIS SERIES OR ANY OF THE CHARACTERS!**

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><p><strong>Jace POV<strong>

****Jace held onto the tightly as Simon sped around the corner. He knew Simon was going as fast as he could, but was still anxious to be there already. "How much longer mundane?" He snapped.

"We're here!" Simon replied getting out of the van. It was a yellow, beaten vehicle, but the had done the job. They all stood at the back of the van preparing there weapons. All Jace wanted to do was run in and make sure she was ok, but he knew he couldn't help if he wasn't properly prepared.

As they started heading over to the building he noticed Simon following. He spun around blocking Simon's path. "Where do you think you are going?"

Simon glared at him, "Clary is in there." was all he said. Jace rolled his eyes and pointed at him.

"You need to stay in car, keep it running." Simon went to protest, but Jace cut him off. "If she is hurt we are going to need to get her back to the institute as fast as possible. That means we need you to keep the car running." Even though he had said it rudely both boys shared a look of understanding.

They approached the house carefully scanning for demonic levels. "They're low." Jace said putting away his sensor. They were by the front door when the sensor began to vibrate violently, just as he was about to say something they heard a high pitch scream followed by a thunder like noise. "Clary!" Jace yelled and raced inside.

As soon as they were inside the door slammed shut. In the middle of the foyer stood an enormous demon. The creature's flesh was livid and bruised-looking. Through the seeping skin, bones protruded—not new white bones, but bones that looked as if they had been in the earth a thousand years, black and cracked and filthy. Its fingers were stripped and skeletal, its thin-fleshed arms pocked with dripping black sores through which more yellowing bone was visible. Its face was a skull, its nose and eyes caved-in holes. Its taloned fingers brushed the floor. Tangled around its wrists and shoulders were bright swatches of cloth: all that remained of Madame Dorothea's silk scarves and turban. It was at least nine feet tall.

It looked down at something they couldn't quite see, with empty eye sockets. "Give me," it said, in a voice like the wind blowing trash across empty pavement, "the Mortal Cup. Give it to me, and I will let you live."

Alec whispered to Jace in a choked voice, "But you said there wasn't much demonic activity—you said the levels were low!"

"They were low," Jace growled.

"Your version of low must be different from mine!" Alec shouted, as the thing turned to look at them. Just past it he could see Clary huddled on the floor. She was clinging to a gold cup and blood was slowly running down her face from a gash on her forehead. Jace sucked in a shaky breath, _this is all my fault, _he thought.

"What are you?" he asked, voice steady, though he felt more rattled seeing Clary hurt.

The thing inclined its head. "I am Abbadon. I am the Demon of the Abyss. Mine are the empty places between the worlds. Mine is the wind and the howling darkness. I am as unlike those mewling things you call demons as an eagle is unlike a fly. You cannot hope to defeat me. Give me the Cup or die."

Isabelle's whip trembled. "It's a Greater Demon," she said. "Jace, if we—"

"What about Dorothea?" Clary's voice came shrilly out of her mouth, Jace winced hearing her sound so scared, yet trying to be brave. "What happened to her?"

The demon's empty eyes swung to regard her. "She was a vessel only," it said. "She opened the Portal and I took possession of her. Her death was swift." Its gaze moved to the Cup in her hand. "Yours will not be."

It began to move toward her. Jace blocked its way, the glittering sword in one hand, a seraph blade appearing in the other. Alec was watching him, his expression sick with horror.

"By the Angel," Jace said, looking the demon up and down. "I knew Greater Demons were meant to be ugly, but no one ever warned me about the smell.

"  
>Abbadon opened its mouth and hissed. Inside its mouth were two rows of jagged glass-sharp teeth.<p>

"I'm not so sure about this wind and howling darkness business," Jace went on, "smells more like landfill to me. You sure you're not from Staten Island?" He couldn't help, but antagonise it.

The demon leaped at him. Jace whipped his blades up and outward with an almost frightening speed; both sank into the fleshiest part of the demon, its abdomen. It howled and struck at him, knocking him aside the way a cat might bat aside a kitten. Jace rolled and got to his feet, he tried to ignore the pain in his arm. He didn't want them to think that he'd been hurt.

That was enough for Isabelle. Darting forward, she lashed out at the demon with her whip. It struck the demon's gray hide, and a red weal appeared, welling blood. Abbadon ignored her, moving toward Jace.

With his uninjured hand Jace drew out a second seraph blade. He whispered to it and it sprung free, bright and gleaming. He raised it as the demon loomed up before him; he refused to show weakness, he grinned at it, not letting any fear show, even as the demon reached for him. Isabelle, screaming, lashed at it, sending blood in a thick spray across the floor—

The demon struck, its razored hand lashing down at Jace. He staggered back, but he was unharmed. Something had thrown itself between him and the demon, a slim black shadow with a gleaming blade in its hand. Alec. The demon shrieked— Alec's featherstaff had pierced its skin. With a snarl it struck again, bone-talons catching Alec a vicious blow that lifted him off his feet and hurled him against the far wall. He struck with a sickening crunch and slid to the floor.

Isabelle screamed her brother's name. He didn't move. Lowering the whip, she started to run to him. The demon, turning, caught her a backhanded blow that sent her spinning to the ground. Coughing blood, Isabelle started to get to her feet; Abbadon knocked her down again, and this time she lay still.

The demon moved toward Clary.

Jace stood frozen, staring at Alec's crumpled body like someone caught in a dream. Clary screamed as Abbadon neared her, but he couldn't move. All he could think was that he had gotten Alec hurt, perhaps even killed.

Isabelle had clawed her way into a sitting position. Pushing her bloody hair back, she screamed at Jace. He could hear Clary's name in Isabelle's screams and blinking as if slapped awake, spun toward her. He began to run. The demon was to close to Clary for his liking. It reached for her—

But Jace got there first and was knocking Abbadon's hand aside. He flung the seraph blade at the demon; it stuck in the creature's chest, next to the two blades already there. The demon snarled as if the blades were no more than an annoyance. "Shadowhunter," it snarled. "I shall take pleasure in killing you, in hearing your bones crunch as your friend's did—"

Springing onto the banister, Jace flung himself at Abbadon. The force of the jump knocked the demon backward; it staggered, Jace clinging to its back. He seized a seraph blade out of its chest, sending up a spray of ichor, and brought the blade down, again and again, into the demon's back, its shoulders running with black fluid.

Snarling, Abbadon backed toward the wall. Jace had to drop or be crushed. He fell to the ground, landed lightly, and raised the blade again. But Abbadon was too swift for him; its hand lashed out, knocking Jace into the stairs. Jace went down, a circle of talons at his throat.

"Tell them to give me the Cup," Abbadon snarled, talons hovering just above Jace's skin. "Tell them to give it to me and I will let them live."  
>Jace swallowed. "Clary—"<p>

**Clary POV**

Clary looked on in terror as Abbadon one by one took down the Shadowhunters. "Tell them to give me the Cup," Abbadon snarled, talons hovering just above Jace's skin. "Tell them to give it to me and I will let them live."

Jace swallowed. "Clary—"

But Clary would never know what he would have said, because at that moment the front door flew open. For a moment all she saw was brightness. Then, blinking away the fiery afterimage, she saw Simon standing in the open doorway. Simon. She was taken completely by surprise that he was there. She had almost forgotten he existed.

He saw her, crouched on the stairs, and his gaze moved past her and over Abbadon and Jace. He reached back over his shoulder. He was holding Alec's bow, she realized, and the quiver was strapped across his back. He drew an arrow from it, fitted it to the string, and lifted the bow expertly, as if he'd done the same thing a hundred times before.

The arrow sprang free. It made a hot buzzing sound, like a huge bumblebee, as it shot over Abbadon's head, plunged toward the roof—

And shattered the skylight. Dirty black glass fell like rain, and through the broken pane streamed sunlight, quantities of sunlight, great golden bars of it stabbing downward and flooding the foyer with light.

Abbadon screamed and staggered back, shielding its misshapen head with its hands. Jace put a hand to his unharmed throat, staring in disbelief as the demon crumpled, howling, to the floor. Clary half-expected it to burst into flames, but instead it began to fold in on itself. Its legs collapsed toward its torso, its skull crumpling like burning paper, and within the span of a minute it had vanished entirely, leaving only scorch marks behind.  
>Simon lowered the bow. He was blinking behind his glasses, his mouth slightly open. He looked as astonished as Clary felt.<p>

Jace lay on the stairs where the demon had thrown him. He was struggling to sit up as Clary slid down the steps and fell to her knees beside him. "Jace—"

"I'm all right." He sat up, wiping blood from his mouth. He coughed and spit red. "Alec—"

"Your stele," she interrupted, reaching for her pocket. "Do you need it to fix yourself ?"

He looked at her. The sunlight pouring through the shattered skylight lit his face. He looked as if he were holding himself back from something with a terrible effort. "I'm all right," he said again, and pushed her aside, none too gently. He got to his feet, staggered, and nearly fell—the first ungraceful thing she'd ever seen him do. "Alec?"

Clary watched him as he limped across the foyer toward his unconscious friend. Then she zipped the Mortal Cup into the pocket of her hoodie and got to her feet. Isabelle had crawled to her brother's side and was cradling his head in her lap, stroking his hair. His chest rose and fell—slowly, but he was breathing. Simon, leaning against the wall watching them, looked utterly drained. Clary squeezed his hand as she passed him. "Thank you," she whispered. "That was amazing."

"Don't thank me," he said, "thank the archery program at B'nai B'rith summer camp."

"Simon, I don't—"

"Clary!" It was Jace, calling her. "Bring my stele."

Simon let her go reluctantly. She knelt down next to the Shadowhunters, the Mortal Cup thumping heavily against her side. Alec's face was white, freckled with drops of blood, his eyes unnaturally blue. His grip on Jace's wrist left bloody smears. "Did I…," he started, then seemed to see Clary, as if for the first time. There was something in his look she hadn't expected. Triumph. "Did I kill it?"

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><p><strong>As you could probably tell it is now back into the original story with a few differences. hope you guys enjoyed my first fanfic. Please review and let me know your thoughts. Also what do you want me to write next? Let me know.<strong>

**xox**


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